Starting phenix.real_space_refine on Fri Feb 6 11:30:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9og5_70453/02_2026/9og5_70453.cif Found real_map, /net/cci-nas-00/data/ceres_data/9og5_70453/02_2026/9og5_70453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9og5_70453/02_2026/9og5_70453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9og5_70453/02_2026/9og5_70453.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9og5_70453/02_2026/9og5_70453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9og5_70453/02_2026/9og5_70453.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.026 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 113 5.16 5 C 15467 2.51 5 N 3974 2.21 5 O 4739 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24293 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 7579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 972, 7579 Classifications: {'peptide': 972} Link IDs: {'PTRANS': 52, 'TRANS': 919} Chain breaks: 11 Chain: "C" Number of atoms: 8010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1024, 8010 Classifications: {'peptide': 1024} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 56, 'TRANS': 967} Chain breaks: 8 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1025, 8008 Classifications: {'peptide': 1025} Link IDs: {'PTRANS': 56, 'TRANS': 968} Chain breaks: 8 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "P" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 98 Unusual residues: {'NAG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 7 Time building chain proxies: 5.93, per 1000 atoms: 0.24 Number of scatterers: 24293 At special positions: 0 Unit cell: (134.784, 134.784, 178.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 113 16.00 O 4739 8.00 N 3974 7.00 C 15467 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=38, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.03 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS C 883 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 883 " - pdb=" SG CYS B 705 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.04 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.03 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.04 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.02 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG O 2 " - " BMA O 3 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " NAG-ASN " NAG A1301 " - " ASN A 17 " " NAG A1302 " - " ASN A 234 " " NAG A1303 " - " ASN A 709 " " NAG A1304 " - " ASN A1134 " " NAG A1305 " - " ASN A 61 " " NAG A1306 " - " ASN A 282 " " NAG B1301 " - " ASN B 234 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 331 " " NAG B1304 " - " ASN B 616 " " NAG B1305 " - " ASN B 657 " " NAG B1306 " - " ASN B 709 " " NAG B1307 " - " ASN B1074 " " NAG C1301 " - " ASN C 331 " " NAG C1302 " - " ASN C 616 " " NAG C1303 " - " ASN C 709 " " NAG C1304 " - " ASN C1074 " " NAG C1305 " - " ASN C 282 " " NAG C1306 " - " ASN C 61 " " NAG D 1 " - " ASN B 343 " " NAG E 1 " - " ASN B 801 " " NAG F 1 " - " ASN B1098 " " NAG G 1 " - " ASN B 717 " " NAG H 1 " - " ASN B1134 " " NAG I 1 " - " ASN C 343 " " NAG J 1 " - " ASN C 717 " " NAG K 1 " - " ASN C 801 " " NAG L 1 " - " ASN C1134 " " NAG M 1 " - " ASN C1098 " " NAG N 1 " - " ASN A 331 " " NAG O 1 " - " ASN A 717 " " NAG P 1 " - " ASN A 801 " " NAG Q 1 " - " ASN A1074 " " NAG R 1 " - " ASN A1098 " Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 1.0 seconds 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5682 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 46 sheets defined 24.3% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 364 through 371 removed outlier: 3.978A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 389 removed outlier: 4.330A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 386 through 389' Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.118A pdb=" N GLU A 406 " --> pdb=" O ARG A 403 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 403 through 407' Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 746 through 754 removed outlier: 3.533A pdb=" N LEU A 752 " --> pdb=" O GLU A 748 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.514A pdb=" N PHE A 782 " --> pdb=" O THR A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 824 Processing helix chain 'A' and resid 849 through 855 removed outlier: 4.024A pdb=" N PHE A 855 " --> pdb=" O CYS A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 866 through 879 Processing helix chain 'A' and resid 879 through 884 removed outlier: 3.982A pdb=" N CYS A 883 " --> pdb=" O ALA A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 886 through 890 removed outlier: 3.620A pdb=" N GLY A 889 " --> pdb=" O TRP A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 897 through 910 Processing helix chain 'A' and resid 912 through 918 removed outlier: 4.427A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 removed outlier: 3.510A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.678A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.697A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'A' and resid 1140 through 1147 removed outlier: 4.476A pdb=" N GLU A1144 " --> pdb=" O PRO A1140 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU A1145 " --> pdb=" O LEU A1141 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 364 through 371 removed outlier: 4.206A pdb=" N LEU C 368 " --> pdb=" O ASP C 364 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 384 through 388 removed outlier: 4.336A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 738 through 743 Processing helix chain 'C' and resid 746 through 751 Processing helix chain 'C' and resid 752 through 757 removed outlier: 4.052A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 782 removed outlier: 3.850A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLN C 779 " --> pdb=" O ASP C 775 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 824 Processing helix chain 'C' and resid 866 through 884 removed outlier: 3.601A pdb=" N ILE C 882 " --> pdb=" O LEU C 878 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS C 883 " --> pdb=" O ALA C 879 " (cutoff:3.500A) Processing helix chain 'C' and resid 897 through 910 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.386A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR C 917 " --> pdb=" O GLN C 913 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 941 Processing helix chain 'C' and resid 945 through 965 Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 982 Processing helix chain 'C' and resid 985 through 1033 Processing helix chain 'C' and resid 1141 through 1146 Processing helix chain 'B' and resid 294 through 303 Processing helix chain 'B' and resid 338 through 342 Processing helix chain 'B' and resid 364 through 371 removed outlier: 3.867A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 384 through 389 removed outlier: 3.748A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 439 through 442 Processing helix chain 'B' and resid 502 through 506 Processing helix chain 'B' and resid 542 through 546 removed outlier: 3.610A pdb=" N GLY B 545 " --> pdb=" O ASN B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 743 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 758 through 782 removed outlier: 3.898A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 779 " --> pdb=" O ASP B 775 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N PHE B 782 " --> pdb=" O THR B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 826 Processing helix chain 'B' and resid 849 through 855 Processing helix chain 'B' and resid 866 through 884 removed outlier: 3.526A pdb=" N ILE B 882 " --> pdb=" O LEU B 878 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N CYS B 883 " --> pdb=" O ALA B 879 " (cutoff:3.500A) Processing helix chain 'B' and resid 886 through 891 removed outlier: 3.832A pdb=" N ALA B 890 " --> pdb=" O TRP B 886 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 891 " --> pdb=" O THR B 887 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 886 through 891' Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 912 through 918 removed outlier: 4.383A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 941 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.658A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) Processing helix chain 'B' and resid 976 through 982 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.153A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) Processing helix chain 'B' and resid 1141 through 1145 removed outlier: 3.523A pdb=" N LEU B1145 " --> pdb=" O GLN B1142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 30 removed outlier: 8.255A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 6.047A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N PHE A 65 " --> pdb=" O TYR A 265 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N TYR A 265 " --> pdb=" O PHE A 65 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 36 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.651A pdb=" N ASP A 53 " --> pdb=" O ARG A 273 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 289 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 85 removed outlier: 3.580A pdb=" N LEU A 241 " --> pdb=" O GLY A 103 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 111 through 121 removed outlier: 6.175A pdb=" N THR A 114 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N PHE A 133 " --> pdb=" O THR A 114 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N CYS A 131 " --> pdb=" O SER A 116 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER A 172 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N PHE A 168 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 5.950A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 317 removed outlier: 6.847A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392 removed outlier: 3.616A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 551 through 554 removed outlier: 4.349A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.594A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.724A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 711 through 722 removed outlier: 6.724A pdb=" N GLN A1071 " --> pdb=" O THR A 716 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N PHE A 718 " --> pdb=" O PRO A1069 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE A 720 " --> pdb=" O TYR A1067 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N TYR A1067 " --> pdb=" O ILE A 720 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N VAL A 722 " --> pdb=" O VAL A1065 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL A1065 " --> pdb=" O VAL A 722 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AB3, first strand: chain 'A' and resid 787 through 788 Processing sheet with id=AB4, first strand: chain 'A' and resid 1120 through 1125 removed outlier: 4.808A pdb=" N ALA A1087 " --> pdb=" O SER A1123 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS A1082 " --> pdb=" O VAL A1133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 1094 through 1098 removed outlier: 4.571A pdb=" N GLN A1106 " --> pdb=" O GLU A1111 " (cutoff:3.500A) removed outlier: 5.333A pdb=" N GLU A1111 " --> pdb=" O GLN A1106 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 27 through 30 removed outlier: 3.861A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 48 through 55 removed outlier: 3.564A pdb=" N VAL C 289 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 84 through 85 Processing sheet with id=AB9, first strand: chain 'C' and resid 224 through 229 removed outlier: 5.742A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL C 227 " --> pdb=" O ILE C 203 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 311 through 314 removed outlier: 3.766A pdb=" N GLY C 648 " --> pdb=" O THR C 645 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.702A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 324 through 326 removed outlier: 7.702A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) removed outlier: 8.492A pdb=" N ASN C 542 " --> pdb=" O GLU C 324 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N ILE C 326 " --> pdb=" O ASN C 542 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 354 through 357 removed outlier: 3.539A pdb=" N SER C 514 " --> pdb=" O TYR C 396 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLY C 431 " --> pdb=" O CYS C 379 " (cutoff:3.500A) removed outlier: 4.801A pdb=" N CYS C 379 " --> pdb=" O GLY C 431 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL C 433 " --> pdb=" O PHE C 377 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE C 377 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'C' and resid 452 through 453 Processing sheet with id=AC6, first strand: chain 'C' and resid 654 through 655 removed outlier: 5.994A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.568A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 701 through 702 removed outlier: 6.399A pdb=" N ALA C 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC7 Processing sheet with id=AC8, first strand: chain 'C' and resid 711 through 722 removed outlier: 6.872A pdb=" N GLN C1071 " --> pdb=" O THR C 716 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE C 718 " --> pdb=" O PRO C1069 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ILE C 720 " --> pdb=" O TYR C1067 " (cutoff:3.500A) removed outlier: 7.077A pdb=" N TYR C1067 " --> pdb=" O ILE C 720 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL C 722 " --> pdb=" O VAL C1065 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N VAL C1065 " --> pdb=" O VAL C 722 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 725 through 728 Processing sheet with id=AD1, first strand: chain 'C' and resid 734 through 736 Processing sheet with id=AD2, first strand: chain 'C' and resid 1081 through 1082 removed outlier: 5.601A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 1094 through 1097 Processing sheet with id=AD4, first strand: chain 'B' and resid 29 through 30 removed outlier: 3.877A pdb=" N THR B 63 " --> pdb=" O VAL B 267 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL B 267 " --> pdb=" O THR B 63 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'B' and resid 36 through 37 removed outlier: 7.076A pdb=" N VAL B 36 " --> pdb=" O LEU B 223 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.621A pdb=" N VAL B 47 " --> pdb=" O TYR B 279 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 90 through 92 removed outlier: 3.561A pdb=" N LYS B 195 " --> pdb=" O LYS B 202 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 116 through 118 removed outlier: 3.592A pdb=" N GLN B 239 " --> pdb=" O ILE B 105 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'B' and resid 311 through 314 Processing sheet with id=AE1, first strand: chain 'B' and resid 324 through 325 removed outlier: 7.687A pdb=" N GLU B 324 " --> pdb=" O ASN B 540 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.718A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 5.118A pdb=" N GLU B 516 " --> pdb=" O ASN B 394 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'B' and resid 357 through 358 removed outlier: 3.718A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N PHE B 392 " --> pdb=" O VAL B 524 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 524 " --> pdb=" O PHE B 392 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'B' and resid 376 through 379 Processing sheet with id=AE5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AE6, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.123A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.594A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.923A pdb=" N GLN B1071 " --> pdb=" O THR B 716 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N PHE B 718 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE B 720 " --> pdb=" O TYR B1067 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR B1067 " --> pdb=" O ILE B 720 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N VAL B 722 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B1065 " --> pdb=" O VAL B 722 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N THR B 724 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B1063 " --> pdb=" O THR B 724 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 726 " --> pdb=" O VAL B1061 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B1061 " --> pdb=" O ILE B 726 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N GLY B1059 " --> pdb=" O PRO B 728 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N MET B1050 " --> pdb=" O VAL B1065 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.548A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'B' and resid 1120 through 1122 Processing sheet with id=AF1, first strand: chain 'B' and resid 1094 through 1097 805 hydrogen bonds defined for protein. 2199 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.57 Time building geometry restraints manager: 2.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7669 1.34 - 1.47: 6221 1.47 - 1.59: 10804 1.59 - 1.71: 0 1.71 - 1.84: 138 Bond restraints: 24832 Sorted by residual: bond pdb=" N PHE A 338 " pdb=" CA PHE A 338 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.15e-02 7.56e+03 8.48e+00 bond pdb=" C VAL B 620 " pdb=" N PRO B 621 " ideal model delta sigma weight residual 1.331 1.364 -0.033 1.20e-02 6.94e+03 7.63e+00 bond pdb=" N VAL A 341 " pdb=" CA VAL A 341 " ideal model delta sigma weight residual 1.459 1.492 -0.033 1.25e-02 6.40e+03 6.96e+00 bond pdb=" N ASN A 331 " pdb=" CA ASN A 331 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.25e-02 6.40e+03 5.97e+00 bond pdb=" N ASN C 165 " pdb=" CA ASN C 165 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.34e+00 ... (remaining 24827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 33355 2.17 - 4.33: 383 4.33 - 6.50: 45 6.50 - 8.67: 14 8.67 - 10.83: 2 Bond angle restraints: 33799 Sorted by residual: angle pdb=" N PRO A 337 " pdb=" CA PRO A 337 " pdb=" C PRO A 337 " ideal model delta sigma weight residual 113.47 104.49 8.98 1.43e+00 4.89e-01 3.95e+01 angle pdb=" N GLY C 526 " pdb=" CA GLY C 526 " pdb=" C GLY C 526 " ideal model delta sigma weight residual 112.10 117.89 -5.79 1.23e+00 6.61e-01 2.22e+01 angle pdb=" C SER B 477 " pdb=" N THR B 478 " pdb=" CA THR B 478 " ideal model delta sigma weight residual 121.80 132.63 -10.83 2.44e+00 1.68e-01 1.97e+01 angle pdb=" C THR C 167 " pdb=" N PHE C 168 " pdb=" CA PHE C 168 " ideal model delta sigma weight residual 122.93 116.64 6.29 1.51e+00 4.39e-01 1.73e+01 angle pdb=" CA ASP C 745 " pdb=" CB ASP C 745 " pdb=" CG ASP C 745 " ideal model delta sigma weight residual 112.60 116.49 -3.89 1.00e+00 1.00e+00 1.51e+01 ... (remaining 33794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 13219 17.97 - 35.94: 1663 35.94 - 53.92: 477 53.92 - 71.89: 91 71.89 - 89.86: 32 Dihedral angle restraints: 15482 sinusoidal: 6682 harmonic: 8800 Sorted by residual: dihedral pdb=" CB CYS B1082 " pdb=" SG CYS B1082 " pdb=" SG CYS B1126 " pdb=" CB CYS B1126 " ideal model delta sinusoidal sigma weight residual 93.00 7.78 85.22 1 1.00e+01 1.00e-02 8.80e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual -86.00 -153.37 67.37 1 1.00e+01 1.00e-02 5.91e+01 dihedral pdb=" CB CYS B 538 " pdb=" SG CYS B 538 " pdb=" SG CYS B 590 " pdb=" CB CYS B 590 " ideal model delta sinusoidal sigma weight residual -86.00 -152.13 66.13 1 1.00e+01 1.00e-02 5.72e+01 ... (remaining 15479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 3586 0.078 - 0.156: 402 0.156 - 0.233: 11 0.233 - 0.311: 0 0.311 - 0.389: 3 Chirality restraints: 4002 Sorted by residual: chirality pdb=" C1 NAG B1301 " pdb=" ND2 ASN B 234 " pdb=" C2 NAG B1301 " pdb=" O5 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN B1098 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.63e+00 chirality pdb=" C1 NAG I 1 " pdb=" ND2 ASN C 343 " pdb=" C2 NAG I 1 " pdb=" O5 NAG I 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.08 -0.32 2.00e-01 2.50e+01 2.59e+00 ... (remaining 3999 not shown) Planarity restraints: 4344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.014 2.00e-02 2.50e+03 1.10e-01 1.50e+02 pdb=" CG ASN A 331 " 0.031 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.082 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " 0.191 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " -0.126 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 138 " 0.045 5.00e-02 4.00e+02 6.83e-02 7.45e+00 pdb=" N PRO B 139 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO B 139 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 139 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 986 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO B 987 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO B 987 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO B 987 " 0.026 5.00e-02 4.00e+02 ... (remaining 4341 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 11248 2.95 - 3.44: 22935 3.44 - 3.92: 39247 3.92 - 4.41: 43598 4.41 - 4.90: 74240 Nonbonded interactions: 191268 Sorted by model distance: nonbonded pdb=" O ASP A 198 " pdb=" OD1 ASP A 198 " model vdw 2.460 3.040 nonbonded pdb=" O GLY A 339 " pdb=" N VAL A 341 " model vdw 2.469 3.120 nonbonded pdb=" C4 NAG O 2 " pdb=" O5 BMA O 3 " model vdw 2.499 2.776 nonbonded pdb=" O ASN B 709 " pdb=" OD1 ASN B 710 " model vdw 2.508 3.040 nonbonded pdb=" O SER C 746 " pdb=" OG SER C 746 " model vdw 2.546 3.040 ... (remaining 191263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 66 or resid 80 through 140 or resid 156 through \ 175 or resid 187 through 243 or resid 263 through 621 or resid 636 through 827 \ or resid 853 through 1145 or resid 1301 through 1306)) selection = (chain 'B' and (resid 26 through 66 or resid 80 through 175 or resid 187 through \ 396 or resid 400 through 412 or resid 429 through 441 or resid 494 through 515 \ or resid 522 through 621 or resid 636 through 827 or resid 853 through 1145 or r \ esid 1302 through 1307)) selection = (chain 'C' and (resid 26 through 66 or resid 80 through 140 or resid 156 through \ 175 or resid 187 through 243 or resid 263 through 396 or resid 400 through 412 \ or resid 429 through 441 or resid 494 through 515 or resid 522 through 676 or re \ sid 689 through 1145 or resid 1301 through 1306)) } ncs_group { reference = (chain 'D' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'E' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'F' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'G' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'H' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'I' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'J' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'K' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'L' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'M' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'N' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = chain 'P' selection = (chain 'Q' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) selection = (chain 'R' and (resid 1 or (resid 2 and (name C1 or name C2 or name C3 or name C \ 4 or name C5 or name C6 or name C7 or name C8 or name N2 or name O3 or name O4 o \ r name O5 or name O6 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.210 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.111 24920 Z= 0.133 Angle : 0.614 27.321 34025 Z= 0.307 Chirality : 0.045 0.389 4002 Planarity : 0.004 0.068 4310 Dihedral : 17.027 89.861 9686 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.40 % Favored : 92.27 % Rotamer: Outliers : 4.14 % Allowed : 27.38 % Favored : 68.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.27 (0.16), residues: 2961 helix: 2.10 (0.21), residues: 621 sheet: -1.21 (0.23), residues: 549 loop : -1.90 (0.14), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 273 TYR 0.012 0.001 TYR B1067 PHE 0.015 0.001 PHE A 927 TRP 0.010 0.001 TRP A 886 HIS 0.003 0.000 HIS B1048 Details of bonding type rmsd covalent geometry : bond 0.00247 (24832) covalent geometry : angle 0.57074 (33799) SS BOND : bond 0.00377 ( 38) SS BOND : angle 1.10738 ( 76) hydrogen bonds : bond 0.19097 ( 799) hydrogen bonds : angle 8.17550 ( 2199) link_BETA1-4 : bond 0.00420 ( 16) link_BETA1-4 : angle 2.00369 ( 48) link_NAG-ASN : bond 0.01947 ( 34) link_NAG-ASN : angle 3.85369 ( 102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 208 time to evaluate : 0.762 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2623 (OUTLIER) cc_final: 0.1712 (mm110) REVERT: A 53 ASP cc_start: 0.7864 (t0) cc_final: 0.7534 (t0) REVERT: A 96 GLU cc_start: 0.6424 (OUTLIER) cc_final: 0.6064 (mt-10) REVERT: A 214 ARG cc_start: 0.5777 (OUTLIER) cc_final: 0.5041 (mmm160) REVERT: A 220 PHE cc_start: 0.7660 (t80) cc_final: 0.7231 (t80) REVERT: A 342 PHE cc_start: 0.5867 (OUTLIER) cc_final: 0.4763 (p90) REVERT: A 531 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8189 (p) REVERT: A 748 GLU cc_start: 0.8377 (mp0) cc_final: 0.7995 (mp0) REVERT: A 821 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8164 (mp) REVERT: A 957 GLN cc_start: 0.7841 (mp10) cc_final: 0.7439 (mt0) REVERT: C 53 ASP cc_start: 0.8234 (t70) cc_final: 0.7913 (t0) REVERT: C 102 ARG cc_start: 0.6863 (mmp80) cc_final: 0.6608 (mmp80) REVERT: C 392 PHE cc_start: 0.6768 (m-80) cc_final: 0.6420 (m-80) REVERT: C 408 ARG cc_start: 0.5643 (mtm180) cc_final: 0.4884 (mtt90) REVERT: C 428 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7754 (p0) REVERT: C 457 ARG cc_start: 0.6215 (OUTLIER) cc_final: 0.5210 (ttm170) REVERT: C 465 GLU cc_start: 0.8461 (pt0) cc_final: 0.8226 (pp20) REVERT: C 983 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7649 (mtm110) REVERT: C 1029 MET cc_start: 0.9038 (OUTLIER) cc_final: 0.8702 (ttm) REVERT: C 1072 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: B 83 VAL cc_start: 0.5384 (OUTLIER) cc_final: 0.5096 (p) REVERT: B 169 GLU cc_start: 0.7661 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: B 220 PHE cc_start: 0.5449 (OUTLIER) cc_final: 0.4939 (t80) REVERT: B 586 ASP cc_start: 0.5824 (t0) cc_final: 0.5609 (t0) REVERT: B 774 GLN cc_start: 0.8623 (mm-40) cc_final: 0.8323 (mp10) REVERT: B 851 CYS cc_start: 0.6296 (OUTLIER) cc_final: 0.5589 (p) REVERT: B 1010 GLN cc_start: 0.8278 (OUTLIER) cc_final: 0.6912 (mp10) REVERT: B 1105 THR cc_start: 0.9405 (OUTLIER) cc_final: 0.9117 (t) REVERT: B 1139 ASP cc_start: 0.8114 (t0) cc_final: 0.7679 (t0) outliers start: 110 outliers final: 77 residues processed: 299 average time/residue: 0.1446 time to fit residues: 70.1251 Evaluate side-chains 293 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 200 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 711 SER Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 873 TYR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 167 THR Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 642 VAL Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 963 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1029 MET Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1104 VAL Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 0.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 616 ASN C1010 GLN B 121 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 439 ASN B 907 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.184778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117175 restraints weight = 31229.330| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 2.66 r_work: 0.3143 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 24920 Z= 0.264 Angle : 0.675 19.764 34025 Z= 0.331 Chirality : 0.049 0.565 4002 Planarity : 0.004 0.057 4310 Dihedral : 8.313 78.647 4434 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.30 % Allowed : 9.63 % Favored : 90.07 % Rotamer: Outliers : 7.80 % Allowed : 24.18 % Favored : 68.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.15), residues: 2961 helix: 1.63 (0.21), residues: 630 sheet: -1.10 (0.21), residues: 622 loop : -2.06 (0.14), residues: 1709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 273 TYR 0.019 0.002 TYR A1067 PHE 0.023 0.002 PHE B 927 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00651 (24832) covalent geometry : angle 0.63912 (33799) SS BOND : bond 0.00568 ( 38) SS BOND : angle 1.39021 ( 76) hydrogen bonds : bond 0.05508 ( 799) hydrogen bonds : angle 6.17693 ( 2199) link_BETA1-4 : bond 0.00334 ( 16) link_BETA1-4 : angle 2.06160 ( 48) link_NAG-ASN : bond 0.00496 ( 34) link_NAG-ASN : angle 3.65438 ( 102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 409 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 207 poor density : 202 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2868 (OUTLIER) cc_final: 0.1945 (mm110) REVERT: A 214 ARG cc_start: 0.5824 (OUTLIER) cc_final: 0.5091 (mmm160) REVERT: A 220 PHE cc_start: 0.7898 (t80) cc_final: 0.7611 (t80) REVERT: A 316 SER cc_start: 0.8658 (m) cc_final: 0.8400 (p) REVERT: A 342 PHE cc_start: 0.5828 (OUTLIER) cc_final: 0.4742 (p90) REVERT: A 644 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.6866 (tm-30) REVERT: A 714 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8927 (mm) REVERT: A 747 THR cc_start: 0.8505 (m) cc_final: 0.8302 (p) REVERT: A 748 GLU cc_start: 0.8382 (mp0) cc_final: 0.8036 (mp0) REVERT: A 821 LEU cc_start: 0.8809 (tt) cc_final: 0.8294 (mp) REVERT: A 957 GLN cc_start: 0.7906 (OUTLIER) cc_final: 0.7518 (mt0) REVERT: C 52 GLN cc_start: 0.8437 (tm-30) cc_final: 0.8088 (tm-30) REVERT: C 129 LYS cc_start: 0.7546 (OUTLIER) cc_final: 0.7331 (tptm) REVERT: C 237 ARG cc_start: 0.8094 (ptm160) cc_final: 0.7332 (ptm160) REVERT: C 278 LYS cc_start: 0.8800 (OUTLIER) cc_final: 0.8532 (tttp) REVERT: C 390 LEU cc_start: 0.8726 (mt) cc_final: 0.8499 (mt) REVERT: C 392 PHE cc_start: 0.7324 (m-80) cc_final: 0.6958 (m-80) REVERT: C 428 ASP cc_start: 0.8296 (OUTLIER) cc_final: 0.7976 (p0) REVERT: C 429 PHE cc_start: 0.7756 (t80) cc_final: 0.7447 (t80) REVERT: C 453 TYR cc_start: 0.6112 (p90) cc_final: 0.5911 (p90) REVERT: C 456 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.5630 (p90) REVERT: C 457 ARG cc_start: 0.6270 (OUTLIER) cc_final: 0.4976 (ttm170) REVERT: C 465 GLU cc_start: 0.8580 (pt0) cc_final: 0.7957 (pp20) REVERT: C 537 LYS cc_start: 0.8109 (OUTLIER) cc_final: 0.7501 (mtpp) REVERT: C 591 SER cc_start: 0.8292 (OUTLIER) cc_final: 0.7908 (p) REVERT: C 779 GLN cc_start: 0.8342 (OUTLIER) cc_final: 0.8073 (tm-30) REVERT: C 895 GLN cc_start: 0.8876 (OUTLIER) cc_final: 0.8534 (pt0) REVERT: C 921 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.8251 (mppt) REVERT: C 983 ARG cc_start: 0.7985 (ttp80) cc_final: 0.7672 (ttm170) REVERT: C 1072 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7733 (mp0) REVERT: B 83 VAL cc_start: 0.5279 (OUTLIER) cc_final: 0.4941 (p) REVERT: B 169 GLU cc_start: 0.7466 (OUTLIER) cc_final: 0.6941 (mp0) REVERT: B 266 TYR cc_start: 0.6255 (OUTLIER) cc_final: 0.5753 (m-80) REVERT: B 393 THR cc_start: 0.9012 (OUTLIER) cc_final: 0.8676 (p) REVERT: B 517 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6951 (mm) REVERT: B 636 TYR cc_start: 0.7450 (OUTLIER) cc_final: 0.7149 (t80) REVERT: B 794 ILE cc_start: 0.7242 (OUTLIER) cc_final: 0.6731 (pt) REVERT: B 851 CYS cc_start: 0.6614 (OUTLIER) cc_final: 0.6204 (p) REVERT: B 907 ASN cc_start: 0.9021 (OUTLIER) cc_final: 0.8783 (m-40) REVERT: B 1010 GLN cc_start: 0.8161 (OUTLIER) cc_final: 0.6793 (mp10) REVERT: B 1028 LYS cc_start: 0.9118 (OUTLIER) cc_final: 0.8552 (mtpp) REVERT: B 1031 GLU cc_start: 0.8906 (OUTLIER) cc_final: 0.8390 (mt-10) REVERT: B 1139 ASP cc_start: 0.8239 (t0) cc_final: 0.7852 (t0) outliers start: 207 outliers final: 135 residues processed: 387 average time/residue: 0.1392 time to fit residues: 88.8939 Evaluate side-chains 355 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 191 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 51 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 574 ASP Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 761 THR Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 961 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1097 SER Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 656 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 732 THR Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 546 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 572 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 CYS Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1105 THR Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 133 optimal weight: 5.9990 chunk 149 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 0.5980 chunk 168 optimal weight: 1.9990 chunk 130 optimal weight: 10.0000 chunk 240 optimal weight: 10.0000 chunk 231 optimal weight: 9.9990 chunk 125 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 241 optimal weight: 0.0570 overall best weight: 1.4902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.183930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.117483 restraints weight = 30909.650| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.54 r_work: 0.3207 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24920 Z= 0.169 Angle : 0.617 20.089 34025 Z= 0.299 Chirality : 0.047 0.530 4002 Planarity : 0.004 0.050 4310 Dihedral : 7.846 76.281 4392 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.71 % Favored : 90.95 % Rotamer: Outliers : 7.38 % Allowed : 24.07 % Favored : 68.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.38 (0.15), residues: 2961 helix: 1.83 (0.21), residues: 624 sheet: -1.02 (0.21), residues: 615 loop : -2.03 (0.14), residues: 1722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 319 TYR 0.016 0.001 TYR A1067 PHE 0.018 0.001 PHE B 86 TRP 0.008 0.001 TRP A 886 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00408 (24832) covalent geometry : angle 0.57898 (33799) SS BOND : bond 0.00435 ( 38) SS BOND : angle 1.43423 ( 76) hydrogen bonds : bond 0.04731 ( 799) hydrogen bonds : angle 5.76081 ( 2199) link_BETA1-4 : bond 0.00353 ( 16) link_BETA1-4 : angle 2.02724 ( 48) link_NAG-ASN : bond 0.00503 ( 34) link_NAG-ASN : angle 3.53313 ( 102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 398 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 196 poor density : 202 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2848 (OUTLIER) cc_final: 0.1925 (mm110) REVERT: A 129 LYS cc_start: 0.7364 (tttp) cc_final: 0.7022 (ttmm) REVERT: A 214 ARG cc_start: 0.5809 (OUTLIER) cc_final: 0.5103 (mmm160) REVERT: A 342 PHE cc_start: 0.5812 (OUTLIER) cc_final: 0.4738 (p90) REVERT: A 714 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.8938 (mm) REVERT: A 747 THR cc_start: 0.8496 (m) cc_final: 0.8278 (p) REVERT: A 748 GLU cc_start: 0.8495 (mp0) cc_final: 0.8135 (mp0) REVERT: A 821 LEU cc_start: 0.8820 (tt) cc_final: 0.8318 (mp) REVERT: A 957 GLN cc_start: 0.8087 (OUTLIER) cc_final: 0.7686 (mt0) REVERT: C 52 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8153 (tm-30) REVERT: C 129 LYS cc_start: 0.7698 (OUTLIER) cc_final: 0.7467 (tptm) REVERT: C 237 ARG cc_start: 0.8130 (ptm160) cc_final: 0.7392 (ptm160) REVERT: C 392 PHE cc_start: 0.7374 (m-80) cc_final: 0.6958 (m-80) REVERT: C 428 ASP cc_start: 0.8318 (OUTLIER) cc_final: 0.8008 (p0) REVERT: C 429 PHE cc_start: 0.7872 (t80) cc_final: 0.7581 (t80) REVERT: C 456 PHE cc_start: 0.6455 (OUTLIER) cc_final: 0.5635 (p90) REVERT: C 457 ARG cc_start: 0.6314 (OUTLIER) cc_final: 0.5044 (ttm170) REVERT: C 465 GLU cc_start: 0.8625 (pt0) cc_final: 0.8022 (pp20) REVERT: C 591 SER cc_start: 0.8367 (OUTLIER) cc_final: 0.7907 (p) REVERT: C 779 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.8150 (tm-30) REVERT: C 895 GLN cc_start: 0.8911 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: C 983 ARG cc_start: 0.8016 (ttp80) cc_final: 0.7665 (ttm170) REVERT: C 1072 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.8025 (mp0) REVERT: B 83 VAL cc_start: 0.5267 (OUTLIER) cc_final: 0.4945 (p) REVERT: B 129 LYS cc_start: 0.7162 (OUTLIER) cc_final: 0.6706 (pttp) REVERT: B 169 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.6948 (mp0) REVERT: B 220 PHE cc_start: 0.5979 (OUTLIER) cc_final: 0.5406 (t80) REVERT: B 266 TYR cc_start: 0.6617 (OUTLIER) cc_final: 0.6161 (m-80) REVERT: B 517 LEU cc_start: 0.7240 (OUTLIER) cc_final: 0.6994 (mm) REVERT: B 636 TYR cc_start: 0.7374 (OUTLIER) cc_final: 0.7061 (t80) REVERT: B 794 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6735 (pt) REVERT: B 851 CYS cc_start: 0.6692 (OUTLIER) cc_final: 0.6196 (p) REVERT: B 1010 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7031 (mp10) REVERT: B 1028 LYS cc_start: 0.9126 (OUTLIER) cc_final: 0.8590 (mtpp) REVERT: B 1029 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8579 (ttp) REVERT: B 1031 GLU cc_start: 0.8953 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: B 1139 ASP cc_start: 0.8236 (t0) cc_final: 0.7847 (t0) outliers start: 196 outliers final: 127 residues processed: 373 average time/residue: 0.1352 time to fit residues: 83.4864 Evaluate side-chains 342 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 189 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 116 SER Chi-restraints excluded: chain C residue 129 LYS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 916 LEU Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 400 PHE Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 636 TYR Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 731 MET Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 866 THR Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 883 CYS Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1028 LYS Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1096 VAL Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 292 optimal weight: 0.8980 chunk 198 optimal weight: 0.2980 chunk 239 optimal weight: 20.0000 chunk 297 optimal weight: 0.9990 chunk 269 optimal weight: 0.0570 chunk 264 optimal weight: 4.9990 chunk 263 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 155 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 616 ASN A 907 ASN C 414 GLN C 907 ASN C1010 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.188978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121256 restraints weight = 30954.494| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 2.66 r_work: 0.3245 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.0998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 24920 Z= 0.108 Angle : 0.598 19.638 34025 Z= 0.286 Chirality : 0.046 0.539 4002 Planarity : 0.004 0.047 4310 Dihedral : 7.585 76.665 4385 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.07 % Favored : 91.62 % Rotamer: Outliers : 6.18 % Allowed : 25.39 % Favored : 68.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.16), residues: 2961 helix: 2.27 (0.21), residues: 620 sheet: -0.93 (0.21), residues: 607 loop : -1.95 (0.14), residues: 1734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 319 TYR 0.028 0.001 TYR C 453 PHE 0.020 0.001 PHE A 92 TRP 0.010 0.001 TRP A 886 HIS 0.003 0.000 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00242 (24832) covalent geometry : angle 0.55782 (33799) SS BOND : bond 0.00352 ( 38) SS BOND : angle 1.04365 ( 76) hydrogen bonds : bond 0.03987 ( 799) hydrogen bonds : angle 5.35876 ( 2199) link_BETA1-4 : bond 0.00362 ( 16) link_BETA1-4 : angle 2.03586 ( 48) link_NAG-ASN : bond 0.00607 ( 34) link_NAG-ASN : angle 3.68505 ( 102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 164 poor density : 214 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2820 (OUTLIER) cc_final: 0.1906 (mm110) REVERT: A 96 GLU cc_start: 0.6465 (OUTLIER) cc_final: 0.6097 (mt-10) REVERT: A 129 LYS cc_start: 0.7225 (tttp) cc_final: 0.6881 (ttmm) REVERT: A 214 ARG cc_start: 0.5825 (OUTLIER) cc_final: 0.5122 (mmm160) REVERT: A 342 PHE cc_start: 0.5799 (OUTLIER) cc_final: 0.4745 (p90) REVERT: A 531 THR cc_start: 0.8657 (OUTLIER) cc_final: 0.8263 (p) REVERT: A 748 GLU cc_start: 0.8476 (mp0) cc_final: 0.8114 (mp0) REVERT: A 821 LEU cc_start: 0.8765 (tt) cc_final: 0.8302 (mp) REVERT: A 957 GLN cc_start: 0.8058 (OUTLIER) cc_final: 0.7671 (mt0) REVERT: C 52 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8135 (tm-30) REVERT: C 237 ARG cc_start: 0.8155 (ptm160) cc_final: 0.7414 (ptm160) REVERT: C 428 ASP cc_start: 0.8267 (OUTLIER) cc_final: 0.7955 (p0) REVERT: C 429 PHE cc_start: 0.7889 (t80) cc_final: 0.7587 (t80) REVERT: C 454 ARG cc_start: 0.7306 (tpp80) cc_final: 0.6661 (tpp80) REVERT: C 456 PHE cc_start: 0.6355 (OUTLIER) cc_final: 0.5604 (p90) REVERT: C 457 ARG cc_start: 0.6376 (OUTLIER) cc_final: 0.5227 (ttm170) REVERT: C 465 GLU cc_start: 0.8587 (pt0) cc_final: 0.8300 (pp20) REVERT: C 537 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7477 (mtpp) REVERT: C 591 SER cc_start: 0.8393 (OUTLIER) cc_final: 0.7827 (p) REVERT: C 619 GLU cc_start: 0.7640 (mt-10) cc_final: 0.7239 (mt-10) REVERT: C 779 GLN cc_start: 0.8474 (OUTLIER) cc_final: 0.8222 (tm-30) REVERT: C 895 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8473 (pt0) REVERT: C 983 ARG cc_start: 0.8030 (ttp80) cc_final: 0.7811 (mtm110) REVERT: C 1072 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: C 1145 LEU cc_start: 0.7256 (OUTLIER) cc_final: 0.7013 (mt) REVERT: B 83 VAL cc_start: 0.5382 (OUTLIER) cc_final: 0.5063 (p) REVERT: B 129 LYS cc_start: 0.7106 (OUTLIER) cc_final: 0.6696 (pttp) REVERT: B 169 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7067 (mp0) REVERT: B 191 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8168 (mm-30) REVERT: B 220 PHE cc_start: 0.5739 (OUTLIER) cc_final: 0.5226 (t80) REVERT: B 241 LEU cc_start: 0.8036 (tp) cc_final: 0.7835 (mm) REVERT: B 266 TYR cc_start: 0.6663 (OUTLIER) cc_final: 0.6175 (m-80) REVERT: B 280 ASN cc_start: 0.7920 (OUTLIER) cc_final: 0.7483 (t0) REVERT: B 774 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8554 (mp10) REVERT: B 851 CYS cc_start: 0.6706 (OUTLIER) cc_final: 0.6241 (p) REVERT: B 1010 GLN cc_start: 0.8267 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: B 1029 MET cc_start: 0.9069 (OUTLIER) cc_final: 0.8438 (ttp) REVERT: B 1031 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: B 1139 ASP cc_start: 0.8163 (t0) cc_final: 0.7758 (t0) outliers start: 164 outliers final: 98 residues processed: 355 average time/residue: 0.1492 time to fit residues: 87.4179 Evaluate side-chains 317 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 194 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 907 ASN Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 515 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 271 GLN Chi-restraints excluded: chain B residue 280 ASN Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 110 optimal weight: 7.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 20.0000 chunk 175 optimal weight: 0.4980 chunk 61 optimal weight: 3.9990 chunk 165 optimal weight: 0.2980 chunk 240 optimal weight: 6.9990 chunk 5 optimal weight: 0.0070 chunk 92 optimal weight: 1.9990 chunk 222 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.3602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN C 907 ASN C1010 GLN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.187002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.118772 restraints weight = 30995.494| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 2.54 r_work: 0.3214 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 24920 Z= 0.159 Angle : 0.608 19.283 34025 Z= 0.292 Chirality : 0.047 0.515 4002 Planarity : 0.004 0.046 4310 Dihedral : 7.506 76.402 4371 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 8.58 % Favored : 91.12 % Rotamer: Outliers : 6.44 % Allowed : 25.16 % Favored : 68.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.16), residues: 2961 helix: 2.17 (0.21), residues: 617 sheet: -0.93 (0.21), residues: 602 loop : -1.97 (0.14), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.015 0.001 TYR A1067 PHE 0.016 0.001 PHE B 86 TRP 0.008 0.001 TRP A 436 HIS 0.003 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00387 (24832) covalent geometry : angle 0.56994 (33799) SS BOND : bond 0.00418 ( 38) SS BOND : angle 1.48140 ( 76) hydrogen bonds : bond 0.04296 ( 799) hydrogen bonds : angle 5.28689 ( 2199) link_BETA1-4 : bond 0.00365 ( 16) link_BETA1-4 : angle 2.00334 ( 48) link_NAG-ASN : bond 0.00539 ( 34) link_NAG-ASN : angle 3.45876 ( 102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 199 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2840 (OUTLIER) cc_final: 0.1921 (mm110) REVERT: A 129 LYS cc_start: 0.7261 (tttp) cc_final: 0.6922 (ttmm) REVERT: A 214 ARG cc_start: 0.5823 (OUTLIER) cc_final: 0.5164 (mmm160) REVERT: A 342 PHE cc_start: 0.5766 (OUTLIER) cc_final: 0.4705 (p90) REVERT: A 531 THR cc_start: 0.8639 (OUTLIER) cc_final: 0.8237 (p) REVERT: A 644 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.6905 (tm-30) REVERT: A 748 GLU cc_start: 0.8466 (mp0) cc_final: 0.8116 (mp0) REVERT: A 821 LEU cc_start: 0.8770 (tt) cc_final: 0.8316 (mp) REVERT: A 957 GLN cc_start: 0.8068 (OUTLIER) cc_final: 0.7678 (mt0) REVERT: C 52 GLN cc_start: 0.8458 (tm-30) cc_final: 0.8134 (tm-30) REVERT: C 237 ARG cc_start: 0.8167 (ptm160) cc_final: 0.7454 (ptm160) REVERT: C 428 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7982 (p0) REVERT: C 429 PHE cc_start: 0.7928 (t80) cc_final: 0.7447 (t80) REVERT: C 456 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5593 (p90) REVERT: C 457 ARG cc_start: 0.6368 (OUTLIER) cc_final: 0.5136 (ttm170) REVERT: C 465 GLU cc_start: 0.8625 (pt0) cc_final: 0.8030 (pp20) REVERT: C 537 LYS cc_start: 0.8099 (OUTLIER) cc_final: 0.7487 (mtpp) REVERT: C 779 GLN cc_start: 0.8480 (OUTLIER) cc_final: 0.8210 (tm-30) REVERT: C 895 GLN cc_start: 0.8912 (OUTLIER) cc_final: 0.8540 (pt0) REVERT: C 983 ARG cc_start: 0.8019 (ttp80) cc_final: 0.7811 (ttm170) REVERT: C 1072 GLU cc_start: 0.8501 (OUTLIER) cc_final: 0.8045 (mp0) REVERT: C 1145 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7155 (mt) REVERT: B 83 VAL cc_start: 0.5356 (OUTLIER) cc_final: 0.5045 (p) REVERT: B 129 LYS cc_start: 0.7149 (OUTLIER) cc_final: 0.6714 (pttp) REVERT: B 169 GLU cc_start: 0.7592 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 191 GLU cc_start: 0.8400 (mm-30) cc_final: 0.8152 (mm-30) REVERT: B 220 PHE cc_start: 0.5875 (OUTLIER) cc_final: 0.5360 (t80) REVERT: B 266 TYR cc_start: 0.6664 (OUTLIER) cc_final: 0.6284 (m-80) REVERT: B 303 LEU cc_start: 0.8256 (mm) cc_final: 0.7976 (mm) REVERT: B 774 GLN cc_start: 0.8872 (mm-40) cc_final: 0.8610 (mp10) REVERT: B 794 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6747 (pt) REVERT: B 907 ASN cc_start: 0.9073 (OUTLIER) cc_final: 0.8746 (m110) REVERT: B 1010 GLN cc_start: 0.8257 (OUTLIER) cc_final: 0.6916 (mp10) REVERT: B 1029 MET cc_start: 0.9082 (OUTLIER) cc_final: 0.8581 (ttp) REVERT: B 1031 GLU cc_start: 0.8921 (OUTLIER) cc_final: 0.8288 (mt-10) REVERT: B 1139 ASP cc_start: 0.8175 (t0) cc_final: 0.7801 (t0) outliers start: 171 outliers final: 121 residues processed: 349 average time/residue: 0.1448 time to fit residues: 83.7101 Evaluate side-chains 338 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 145 poor density : 193 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 166 CYS Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 205 SER Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 525 CYS Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain C residue 1145 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 907 ASN Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 262 optimal weight: 1.9990 chunk 135 optimal weight: 10.0000 chunk 12 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 214 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 251 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN A 907 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 280 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.185318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.117099 restraints weight = 31004.047| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 2.64 r_work: 0.3183 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3027 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 24920 Z= 0.194 Angle : 0.632 19.311 34025 Z= 0.305 Chirality : 0.048 0.496 4002 Planarity : 0.004 0.047 4310 Dihedral : 7.607 75.227 4370 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.05 % Favored : 90.61 % Rotamer: Outliers : 6.97 % Allowed : 24.71 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.15), residues: 2961 helix: 1.91 (0.21), residues: 625 sheet: -1.11 (0.20), residues: 633 loop : -1.93 (0.15), residues: 1703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 319 TYR 0.021 0.001 TYR C 453 PHE 0.019 0.001 PHE B 927 TRP 0.014 0.001 TRP A 886 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00476 (24832) covalent geometry : angle 0.59635 (33799) SS BOND : bond 0.00468 ( 38) SS BOND : angle 1.38669 ( 76) hydrogen bonds : bond 0.04643 ( 799) hydrogen bonds : angle 5.32286 ( 2199) link_BETA1-4 : bond 0.00364 ( 16) link_BETA1-4 : angle 2.00408 ( 48) link_NAG-ASN : bond 0.00512 ( 34) link_NAG-ASN : angle 3.49183 ( 102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 185 poor density : 200 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2901 (OUTLIER) cc_final: 0.1978 (mm110) REVERT: A 96 GLU cc_start: 0.6538 (OUTLIER) cc_final: 0.6122 (mt-10) REVERT: A 129 LYS cc_start: 0.7269 (tttp) cc_final: 0.6932 (ttmm) REVERT: A 214 ARG cc_start: 0.5840 (OUTLIER) cc_final: 0.5177 (mmm160) REVERT: A 220 PHE cc_start: 0.7563 (t80) cc_final: 0.6967 (t80) REVERT: A 316 SER cc_start: 0.8717 (m) cc_final: 0.8470 (p) REVERT: A 342 PHE cc_start: 0.5732 (OUTLIER) cc_final: 0.4685 (p90) REVERT: A 637 SER cc_start: 0.7702 (OUTLIER) cc_final: 0.7138 (t) REVERT: A 644 GLN cc_start: 0.8923 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: A 748 GLU cc_start: 0.8481 (mp0) cc_final: 0.8126 (mp0) REVERT: A 821 LEU cc_start: 0.8786 (tt) cc_final: 0.8341 (mp) REVERT: A 957 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.7703 (mt0) REVERT: C 52 GLN cc_start: 0.8475 (tm-30) cc_final: 0.8144 (tm-30) REVERT: C 102 ARG cc_start: 0.6827 (mmp80) cc_final: 0.6372 (mmp80) REVERT: C 237 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7436 (ptm160) REVERT: C 278 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8534 (tttp) REVERT: C 428 ASP cc_start: 0.8346 (OUTLIER) cc_final: 0.8041 (p0) REVERT: C 429 PHE cc_start: 0.7937 (t80) cc_final: 0.7669 (t80) REVERT: C 456 PHE cc_start: 0.6489 (OUTLIER) cc_final: 0.5650 (p90) REVERT: C 457 ARG cc_start: 0.6503 (OUTLIER) cc_final: 0.5122 (ttm170) REVERT: C 465 GLU cc_start: 0.8656 (pt0) cc_final: 0.8027 (pp20) REVERT: C 779 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: C 895 GLN cc_start: 0.8938 (OUTLIER) cc_final: 0.8616 (pt0) REVERT: C 921 LYS cc_start: 0.8706 (OUTLIER) cc_final: 0.8286 (mppt) REVERT: C 983 ARG cc_start: 0.8014 (ttp80) cc_final: 0.7673 (ttm170) REVERT: C 1072 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: B 83 VAL cc_start: 0.5335 (OUTLIER) cc_final: 0.4997 (p) REVERT: B 129 LYS cc_start: 0.7179 (OUTLIER) cc_final: 0.6726 (pttp) REVERT: B 169 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7013 (mp0) REVERT: B 200 TYR cc_start: 0.6207 (OUTLIER) cc_final: 0.4825 (m-80) REVERT: B 220 PHE cc_start: 0.5951 (OUTLIER) cc_final: 0.5435 (t80) REVERT: B 238 PHE cc_start: 0.4839 (p90) cc_final: 0.4534 (p90) REVERT: B 266 TYR cc_start: 0.6683 (OUTLIER) cc_final: 0.6412 (m-80) REVERT: B 303 LEU cc_start: 0.8283 (OUTLIER) cc_final: 0.8013 (mm) REVERT: B 392 PHE cc_start: 0.7901 (OUTLIER) cc_final: 0.6932 (p90) REVERT: B 517 LEU cc_start: 0.7167 (OUTLIER) cc_final: 0.6813 (mm) REVERT: B 557 LYS cc_start: 0.8030 (mttt) cc_final: 0.7719 (mttt) REVERT: B 563 GLN cc_start: 0.7447 (mt0) cc_final: 0.7182 (mp10) REVERT: B 794 ILE cc_start: 0.7258 (OUTLIER) cc_final: 0.6732 (pt) REVERT: B 851 CYS cc_start: 0.6695 (OUTLIER) cc_final: 0.6387 (p) REVERT: B 1010 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.7018 (mp10) REVERT: B 1029 MET cc_start: 0.9096 (OUTLIER) cc_final: 0.8641 (ttp) REVERT: B 1031 GLU cc_start: 0.8983 (OUTLIER) cc_final: 0.8371 (mt-10) REVERT: B 1139 ASP cc_start: 0.8217 (t0) cc_final: 0.7838 (t0) outliers start: 185 outliers final: 135 residues processed: 367 average time/residue: 0.1484 time to fit residues: 90.3808 Evaluate side-chains 357 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 192 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 326 ILE Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 530 SER Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 560 LEU Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 724 THR Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 963 VAL Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1072 GLU Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 110 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 278 LYS Chi-restraints excluded: chain C residue 284 THR Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 302 THR Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 517 LEU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 553 THR Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 723 THR Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 911 VAL Chi-restraints excluded: chain C residue 921 LYS Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 976 VAL Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1127 ASP Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 167 THR Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 312 ILE Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 591 SER Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 624 ILE Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 734 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1081 ILE Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1106 GLN Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 32 optimal weight: 10.0000 chunk 42 optimal weight: 0.0970 chunk 43 optimal weight: 0.9980 chunk 255 optimal weight: 4.9990 chunk 168 optimal weight: 0.5980 chunk 253 optimal weight: 9.9990 chunk 48 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 277 optimal weight: 0.9990 chunk 10 optimal weight: 20.0000 chunk 70 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN C 710 ASN C 907 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 280 ASN B 907 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.188238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.120299 restraints weight = 30848.542| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.63 r_work: 0.3243 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24920 Z= 0.115 Angle : 0.592 19.405 34025 Z= 0.284 Chirality : 0.046 0.523 4002 Planarity : 0.004 0.047 4310 Dihedral : 7.362 76.073 4369 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.34 % Allowed : 7.63 % Favored : 92.03 % Rotamer: Outliers : 5.65 % Allowed : 26.14 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.08 (0.16), residues: 2961 helix: 2.30 (0.21), residues: 620 sheet: -0.95 (0.20), residues: 618 loop : -1.87 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 34 TYR 0.018 0.001 TYR A 28 PHE 0.016 0.001 PHE A 927 TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00266 (24832) covalent geometry : angle 0.55399 (33799) SS BOND : bond 0.00386 ( 38) SS BOND : angle 1.47991 ( 76) hydrogen bonds : bond 0.03917 ( 799) hydrogen bonds : angle 5.03549 ( 2199) link_BETA1-4 : bond 0.00376 ( 16) link_BETA1-4 : angle 2.00048 ( 48) link_NAG-ASN : bond 0.00543 ( 34) link_NAG-ASN : angle 3.39847 ( 102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 150 poor density : 208 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2829 (OUTLIER) cc_final: 0.1916 (mm110) REVERT: A 34 ARG cc_start: 0.7817 (mmt180) cc_final: 0.7301 (mmt180) REVERT: A 96 GLU cc_start: 0.6518 (OUTLIER) cc_final: 0.6143 (mt-10) REVERT: A 129 LYS cc_start: 0.7270 (tttp) cc_final: 0.6946 (ttmm) REVERT: A 214 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.5180 (mmm160) REVERT: A 220 PHE cc_start: 0.7406 (t80) cc_final: 0.7128 (t80) REVERT: A 224 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7641 (mt-10) REVERT: A 342 PHE cc_start: 0.5760 (OUTLIER) cc_final: 0.4708 (p90) REVERT: A 644 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.6883 (tm-30) REVERT: A 748 GLU cc_start: 0.8444 (mp0) cc_final: 0.8109 (mp0) REVERT: A 821 LEU cc_start: 0.8742 (tt) cc_final: 0.8316 (mp) REVERT: A 957 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: C 52 GLN cc_start: 0.8416 (tm-30) cc_final: 0.8091 (tm-30) REVERT: C 102 ARG cc_start: 0.6832 (mmp80) cc_final: 0.6611 (mmp80) REVERT: C 237 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7441 (ptm160) REVERT: C 269 TYR cc_start: 0.8191 (m-10) cc_final: 0.7708 (m-10) REVERT: C 428 ASP cc_start: 0.8303 (OUTLIER) cc_final: 0.8000 (p0) REVERT: C 429 PHE cc_start: 0.7931 (t80) cc_final: 0.7663 (t80) REVERT: C 456 PHE cc_start: 0.6464 (OUTLIER) cc_final: 0.5586 (p90) REVERT: C 457 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.5362 (ttm170) REVERT: C 465 GLU cc_start: 0.8629 (pt0) cc_final: 0.8078 (pp20) REVERT: C 537 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7466 (mtpp) REVERT: C 619 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7234 (mt-10) REVERT: C 779 GLN cc_start: 0.8435 (OUTLIER) cc_final: 0.8207 (tm-30) REVERT: C 895 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.8500 (pt0) REVERT: C 983 ARG cc_start: 0.7984 (ttp80) cc_final: 0.7624 (ttm170) REVERT: C 1072 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8027 (mp0) REVERT: B 83 VAL cc_start: 0.5367 (OUTLIER) cc_final: 0.5054 (p) REVERT: B 129 LYS cc_start: 0.7161 (OUTLIER) cc_final: 0.6733 (pttp) REVERT: B 169 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: B 191 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7989 (tp30) REVERT: B 200 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.4910 (m-80) REVERT: B 220 PHE cc_start: 0.5644 (OUTLIER) cc_final: 0.5155 (t80) REVERT: B 266 TYR cc_start: 0.6701 (OUTLIER) cc_final: 0.6404 (m-80) REVERT: B 557 LYS cc_start: 0.7982 (mttt) cc_final: 0.7661 (mttt) REVERT: B 563 GLN cc_start: 0.7423 (mt0) cc_final: 0.7178 (mp10) REVERT: B 774 GLN cc_start: 0.8829 (mm-40) cc_final: 0.8581 (mp10) REVERT: B 794 ILE cc_start: 0.7213 (OUTLIER) cc_final: 0.6753 (pt) REVERT: B 851 CYS cc_start: 0.6839 (OUTLIER) cc_final: 0.6381 (p) REVERT: B 1010 GLN cc_start: 0.8264 (OUTLIER) cc_final: 0.6942 (mp10) REVERT: B 1029 MET cc_start: 0.9049 (OUTLIER) cc_final: 0.8619 (ttp) REVERT: B 1031 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: B 1139 ASP cc_start: 0.8185 (t0) cc_final: 0.7801 (t0) outliers start: 150 outliers final: 99 residues processed: 337 average time/residue: 0.1482 time to fit residues: 81.9266 Evaluate side-chains 322 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 125 poor density : 197 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 537 LYS Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 666 ILE Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1097 SER Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 116 optimal weight: 0.0050 chunk 239 optimal weight: 0.9990 chunk 68 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 196 optimal weight: 0.7980 chunk 120 optimal weight: 0.6980 chunk 204 optimal weight: 6.9990 chunk 42 optimal weight: 0.3980 chunk 284 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN C 907 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.178461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.112292 restraints weight = 30712.540| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.91 r_work: 0.3080 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2921 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24920 Z= 0.110 Angle : 0.591 19.294 34025 Z= 0.284 Chirality : 0.046 0.524 4002 Planarity : 0.004 0.048 4310 Dihedral : 7.159 77.161 4365 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.34 % Allowed : 8.00 % Favored : 91.66 % Rotamer: Outliers : 4.97 % Allowed : 26.74 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.99 (0.16), residues: 2961 helix: 2.43 (0.21), residues: 621 sheet: -0.88 (0.21), residues: 617 loop : -1.84 (0.15), residues: 1723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 319 TYR 0.018 0.001 TYR C 453 PHE 0.025 0.001 PHE B 238 TRP 0.009 0.001 TRP A 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00254 (24832) covalent geometry : angle 0.55458 (33799) SS BOND : bond 0.00357 ( 38) SS BOND : angle 1.41335 ( 76) hydrogen bonds : bond 0.03770 ( 799) hydrogen bonds : angle 4.92097 ( 2199) link_BETA1-4 : bond 0.00393 ( 16) link_BETA1-4 : angle 1.97673 ( 48) link_NAG-ASN : bond 0.00548 ( 34) link_NAG-ASN : angle 3.38556 ( 102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 206 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2803 (OUTLIER) cc_final: 0.1913 (mm110) REVERT: A 96 GLU cc_start: 0.6432 (OUTLIER) cc_final: 0.6057 (mt-10) REVERT: A 129 LYS cc_start: 0.7080 (tttp) cc_final: 0.6830 (ttmm) REVERT: A 214 ARG cc_start: 0.5723 (OUTLIER) cc_final: 0.5120 (mmm160) REVERT: A 220 PHE cc_start: 0.7319 (t80) cc_final: 0.6926 (t80) REVERT: A 342 PHE cc_start: 0.5670 (OUTLIER) cc_final: 0.4710 (p90) REVERT: A 531 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8180 (p) REVERT: A 644 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.6719 (tm-30) REVERT: A 748 GLU cc_start: 0.8421 (mp0) cc_final: 0.7988 (mp0) REVERT: A 821 LEU cc_start: 0.8655 (tt) cc_final: 0.8191 (mp) REVERT: A 934 ILE cc_start: 0.8975 (OUTLIER) cc_final: 0.8634 (tp) REVERT: A 957 GLN cc_start: 0.8006 (OUTLIER) cc_final: 0.7595 (mt0) REVERT: C 52 GLN cc_start: 0.8407 (tm-30) cc_final: 0.8073 (tm-30) REVERT: C 53 ASP cc_start: 0.8097 (t70) cc_final: 0.7870 (t70) REVERT: C 102 ARG cc_start: 0.6760 (mmp80) cc_final: 0.6512 (mmp80) REVERT: C 237 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7306 (ptm160) REVERT: C 269 TYR cc_start: 0.8100 (m-10) cc_final: 0.7577 (m-10) REVERT: C 428 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7926 (p0) REVERT: C 429 PHE cc_start: 0.7852 (t80) cc_final: 0.7586 (t80) REVERT: C 456 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5549 (p90) REVERT: C 457 ARG cc_start: 0.6510 (OUTLIER) cc_final: 0.5431 (ttm170) REVERT: C 465 GLU cc_start: 0.8555 (pt0) cc_final: 0.7998 (pp20) REVERT: C 779 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8147 (tm-30) REVERT: C 895 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8465 (pt0) REVERT: C 983 ARG cc_start: 0.7995 (ttp80) cc_final: 0.7670 (ttm170) REVERT: C 1072 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: B 83 VAL cc_start: 0.5331 (OUTLIER) cc_final: 0.5017 (p) REVERT: B 129 LYS cc_start: 0.7077 (OUTLIER) cc_final: 0.6618 (pttp) REVERT: B 169 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7009 (mp0) REVERT: B 200 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.4768 (m-80) REVERT: B 220 PHE cc_start: 0.5446 (OUTLIER) cc_final: 0.4960 (t80) REVERT: B 266 TYR cc_start: 0.6673 (OUTLIER) cc_final: 0.6437 (m-80) REVERT: B 347 PHE cc_start: 0.6509 (m-10) cc_final: 0.6216 (m-10) REVERT: B 557 LYS cc_start: 0.7921 (mttt) cc_final: 0.7590 (mttt) REVERT: B 563 GLN cc_start: 0.7336 (mt0) cc_final: 0.7018 (mp10) REVERT: B 774 GLN cc_start: 0.8726 (mm-40) cc_final: 0.8478 (mp10) REVERT: B 851 CYS cc_start: 0.6707 (OUTLIER) cc_final: 0.6250 (p) REVERT: B 1010 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7044 (mp10) REVERT: B 1029 MET cc_start: 0.8952 (OUTLIER) cc_final: 0.8524 (ttp) REVERT: B 1031 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8212 (mt-10) REVERT: B 1139 ASP cc_start: 0.8173 (t0) cc_final: 0.7774 (t0) outliers start: 132 outliers final: 96 residues processed: 320 average time/residue: 0.1526 time to fit residues: 80.2228 Evaluate side-chains 316 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 195 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 569 ILE Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1075 PHE Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 779 GLN Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1018 ILE Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 266 TYR Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 203 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 147 optimal weight: 2.9990 chunk 223 optimal weight: 0.0060 chunk 0 optimal weight: 30.0000 chunk 86 optimal weight: 1.9990 chunk 176 optimal weight: 1.9990 chunk 168 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 127 optimal weight: 7.9990 chunk 97 optimal weight: 10.0000 overall best weight: 1.4602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.186826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.118342 restraints weight = 31050.399| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.52 r_work: 0.3223 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 24920 Z= 0.168 Angle : 0.625 19.338 34025 Z= 0.301 Chirality : 0.047 0.507 4002 Planarity : 0.004 0.047 4310 Dihedral : 7.254 76.400 4364 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.38 % Favored : 91.25 % Rotamer: Outliers : 5.42 % Allowed : 26.29 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.14 (0.16), residues: 2961 helix: 2.22 (0.21), residues: 617 sheet: -0.92 (0.20), residues: 629 loop : -1.92 (0.15), residues: 1715 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 319 TYR 0.015 0.001 TYR A1067 PHE 0.025 0.001 PHE B 238 TRP 0.008 0.001 TRP A 436 HIS 0.004 0.001 HIS B1064 Details of bonding type rmsd covalent geometry : bond 0.00408 (24832) covalent geometry : angle 0.58835 (33799) SS BOND : bond 0.00472 ( 38) SS BOND : angle 1.64458 ( 76) hydrogen bonds : bond 0.04285 ( 799) hydrogen bonds : angle 5.03489 ( 2199) link_BETA1-4 : bond 0.00380 ( 16) link_BETA1-4 : angle 1.95882 ( 48) link_NAG-ASN : bond 0.00509 ( 34) link_NAG-ASN : angle 3.44945 ( 102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 199 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2788 (OUTLIER) cc_final: 0.1929 (mm110) REVERT: A 96 GLU cc_start: 0.6451 (OUTLIER) cc_final: 0.6079 (mt-10) REVERT: A 129 LYS cc_start: 0.7148 (tttp) cc_final: 0.6682 (ttmm) REVERT: A 214 ARG cc_start: 0.5781 (OUTLIER) cc_final: 0.5252 (mmm160) REVERT: A 220 PHE cc_start: 0.7485 (t80) cc_final: 0.7047 (t80) REVERT: A 342 PHE cc_start: 0.5700 (OUTLIER) cc_final: 0.4720 (p90) REVERT: A 637 SER cc_start: 0.7656 (OUTLIER) cc_final: 0.7077 (t) REVERT: A 644 GLN cc_start: 0.8869 (OUTLIER) cc_final: 0.6906 (tm-30) REVERT: A 745 ASP cc_start: 0.7814 (t0) cc_final: 0.7605 (t0) REVERT: A 748 GLU cc_start: 0.8441 (mp0) cc_final: 0.8104 (mp0) REVERT: A 821 LEU cc_start: 0.8749 (tt) cc_final: 0.8294 (mp) REVERT: A 957 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7699 (mt0) REVERT: C 52 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8053 (tm-30) REVERT: C 102 ARG cc_start: 0.6798 (mmp80) cc_final: 0.6535 (mmp80) REVERT: C 237 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7458 (ptm160) REVERT: C 269 TYR cc_start: 0.8187 (m-10) cc_final: 0.7828 (m-10) REVERT: C 428 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7977 (p0) REVERT: C 429 PHE cc_start: 0.7924 (t80) cc_final: 0.7673 (t80) REVERT: C 456 PHE cc_start: 0.6505 (OUTLIER) cc_final: 0.5643 (p90) REVERT: C 457 ARG cc_start: 0.6665 (OUTLIER) cc_final: 0.5437 (ttm170) REVERT: C 465 GLU cc_start: 0.8649 (pt0) cc_final: 0.8063 (pp20) REVERT: C 895 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8561 (pt0) REVERT: C 983 ARG cc_start: 0.7990 (ttp80) cc_final: 0.7709 (ttm170) REVERT: C 1072 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8081 (mp0) REVERT: B 83 VAL cc_start: 0.5431 (OUTLIER) cc_final: 0.5105 (p) REVERT: B 129 LYS cc_start: 0.7188 (OUTLIER) cc_final: 0.6722 (pttp) REVERT: B 169 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.6974 (mp0) REVERT: B 200 TYR cc_start: 0.6129 (OUTLIER) cc_final: 0.4822 (m-80) REVERT: B 220 PHE cc_start: 0.5740 (OUTLIER) cc_final: 0.5183 (t80) REVERT: B 231 ILE cc_start: 0.5778 (OUTLIER) cc_final: 0.5510 (pt) REVERT: B 517 LEU cc_start: 0.7059 (OUTLIER) cc_final: 0.6747 (mm) REVERT: B 557 LYS cc_start: 0.8003 (mttt) cc_final: 0.7644 (mttt) REVERT: B 563 GLN cc_start: 0.7404 (mt0) cc_final: 0.7124 (mp10) REVERT: B 774 GLN cc_start: 0.8875 (mm-40) cc_final: 0.8616 (mp10) REVERT: B 794 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6745 (pt) REVERT: B 851 CYS cc_start: 0.6788 (OUTLIER) cc_final: 0.6370 (p) REVERT: B 1010 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.6898 (mp10) REVERT: B 1029 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8610 (ttp) REVERT: B 1031 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8300 (mt-10) REVERT: B 1139 ASP cc_start: 0.8233 (t0) cc_final: 0.7854 (t0) outliers start: 144 outliers final: 105 residues processed: 323 average time/residue: 0.1416 time to fit residues: 75.9429 Evaluate side-chains 321 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 191 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain A residue 1132 ILE Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 939 SER Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1107 ARG Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 362 VAL Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 794 ILE Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 914 ASN Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1076 THR Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 285 optimal weight: 0.0000 chunk 46 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 299 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 12 optimal weight: 9.9990 chunk 41 optimal weight: 0.9990 chunk 201 optimal weight: 5.9990 chunk 32 optimal weight: 0.2980 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN C 907 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.178405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110224 restraints weight = 30803.971| |-----------------------------------------------------------------------------| r_work (start): 0.3245 rms_B_bonded: 2.95 r_work: 0.3071 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2911 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24920 Z= 0.114 Angle : 0.600 19.444 34025 Z= 0.290 Chirality : 0.046 0.520 4002 Planarity : 0.004 0.047 4310 Dihedral : 7.110 77.418 4364 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.37 % Allowed : 7.63 % Favored : 92.00 % Rotamer: Outliers : 4.82 % Allowed : 26.97 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.16), residues: 2961 helix: 2.33 (0.21), residues: 625 sheet: -0.85 (0.20), residues: 626 loop : -1.81 (0.15), residues: 1710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.012 0.001 TYR C1067 PHE 0.023 0.001 PHE B 238 TRP 0.015 0.001 TRP A 886 HIS 0.002 0.000 HIS A1088 Details of bonding type rmsd covalent geometry : bond 0.00263 (24832) covalent geometry : angle 0.56281 (33799) SS BOND : bond 0.00397 ( 38) SS BOND : angle 1.55517 ( 76) hydrogen bonds : bond 0.03803 ( 799) hydrogen bonds : angle 4.86505 ( 2199) link_BETA1-4 : bond 0.00378 ( 16) link_BETA1-4 : angle 1.96446 ( 48) link_NAG-ASN : bond 0.00545 ( 34) link_NAG-ASN : angle 3.39496 ( 102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5922 Ramachandran restraints generated. 2961 Oldfield, 0 Emsley, 2961 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 128 poor density : 195 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 GLN cc_start: 0.2883 (OUTLIER) cc_final: 0.1978 (mm110) REVERT: A 96 GLU cc_start: 0.6362 (OUTLIER) cc_final: 0.5993 (mt-10) REVERT: A 129 LYS cc_start: 0.7200 (tttp) cc_final: 0.6829 (ttmm) REVERT: A 214 ARG cc_start: 0.5755 (OUTLIER) cc_final: 0.5205 (mmm160) REVERT: A 220 PHE cc_start: 0.7288 (t80) cc_final: 0.6899 (t80) REVERT: A 224 GLU cc_start: 0.7881 (OUTLIER) cc_final: 0.7552 (mt-10) REVERT: A 342 PHE cc_start: 0.5629 (OUTLIER) cc_final: 0.4687 (p90) REVERT: A 531 THR cc_start: 0.8568 (OUTLIER) cc_final: 0.8161 (p) REVERT: A 637 SER cc_start: 0.7785 (OUTLIER) cc_final: 0.7169 (t) REVERT: A 644 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.6745 (tm-30) REVERT: A 745 ASP cc_start: 0.7851 (t0) cc_final: 0.7617 (t0) REVERT: A 748 GLU cc_start: 0.8412 (mp0) cc_final: 0.7973 (mp0) REVERT: A 821 LEU cc_start: 0.8641 (tt) cc_final: 0.8182 (mp) REVERT: A 957 GLN cc_start: 0.8001 (OUTLIER) cc_final: 0.7580 (mt0) REVERT: C 52 GLN cc_start: 0.8364 (tm-30) cc_final: 0.8003 (tm-30) REVERT: C 102 ARG cc_start: 0.6699 (mmp80) cc_final: 0.6441 (mmp80) REVERT: C 237 ARG cc_start: 0.7992 (OUTLIER) cc_final: 0.7279 (ptm160) REVERT: C 269 TYR cc_start: 0.8116 (m-10) cc_final: 0.7659 (m-10) REVERT: C 428 ASP cc_start: 0.8237 (OUTLIER) cc_final: 0.7921 (p0) REVERT: C 429 PHE cc_start: 0.7817 (t80) cc_final: 0.7582 (t80) REVERT: C 456 PHE cc_start: 0.6334 (OUTLIER) cc_final: 0.5459 (p90) REVERT: C 457 ARG cc_start: 0.6509 (OUTLIER) cc_final: 0.5431 (ttm170) REVERT: C 458 LYS cc_start: 0.6928 (OUTLIER) cc_final: 0.6046 (ptpt) REVERT: C 465 GLU cc_start: 0.8548 (pt0) cc_final: 0.7983 (pp20) REVERT: C 895 GLN cc_start: 0.8915 (OUTLIER) cc_final: 0.8457 (pt0) REVERT: C 983 ARG cc_start: 0.8023 (ttp80) cc_final: 0.7696 (ttm170) REVERT: C 1072 GLU cc_start: 0.8506 (OUTLIER) cc_final: 0.8116 (mp0) REVERT: B 83 VAL cc_start: 0.5392 (OUTLIER) cc_final: 0.5059 (p) REVERT: B 129 LYS cc_start: 0.7098 (OUTLIER) cc_final: 0.6635 (pttp) REVERT: B 169 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.6982 (mp0) REVERT: B 200 TYR cc_start: 0.6224 (OUTLIER) cc_final: 0.4953 (m-80) REVERT: B 220 PHE cc_start: 0.5385 (OUTLIER) cc_final: 0.4902 (t80) REVERT: B 231 ILE cc_start: 0.5604 (OUTLIER) cc_final: 0.5354 (pt) REVERT: B 517 LEU cc_start: 0.6939 (OUTLIER) cc_final: 0.6692 (mm) REVERT: B 557 LYS cc_start: 0.7863 (mttt) cc_final: 0.7516 (mttt) REVERT: B 563 GLN cc_start: 0.7340 (mt0) cc_final: 0.7010 (mp10) REVERT: B 651 ILE cc_start: 0.9251 (mp) cc_final: 0.9027 (mm) REVERT: B 774 GLN cc_start: 0.8730 (mm-40) cc_final: 0.8485 (mp10) REVERT: B 851 CYS cc_start: 0.6621 (OUTLIER) cc_final: 0.6189 (p) REVERT: B 1010 GLN cc_start: 0.8326 (OUTLIER) cc_final: 0.7009 (mp10) REVERT: B 1029 MET cc_start: 0.8956 (OUTLIER) cc_final: 0.8587 (ttp) REVERT: B 1031 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: B 1139 ASP cc_start: 0.8210 (t0) cc_final: 0.7814 (t0) outliers start: 128 outliers final: 96 residues processed: 304 average time/residue: 0.1443 time to fit residues: 72.4557 Evaluate side-chains 313 residues out of total 2656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 123 poor density : 190 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 GLN Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 90 VAL Chi-restraints excluded: chain A residue 96 GLU Chi-restraints excluded: chain A residue 140 PHE Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 214 ARG Chi-restraints excluded: chain A residue 224 GLU Chi-restraints excluded: chain A residue 291 CYS Chi-restraints excluded: chain A residue 309 GLU Chi-restraints excluded: chain A residue 312 ILE Chi-restraints excluded: chain A residue 342 PHE Chi-restraints excluded: chain A residue 409 GLN Chi-restraints excluded: chain A residue 512 VAL Chi-restraints excluded: chain A residue 531 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 599 THR Chi-restraints excluded: chain A residue 615 VAL Chi-restraints excluded: chain A residue 624 ILE Chi-restraints excluded: chain A residue 633 TRP Chi-restraints excluded: chain A residue 637 SER Chi-restraints excluded: chain A residue 644 GLN Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 704 SER Chi-restraints excluded: chain A residue 714 ILE Chi-restraints excluded: chain A residue 732 THR Chi-restraints excluded: chain A residue 734 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 874 THR Chi-restraints excluded: chain A residue 887 THR Chi-restraints excluded: chain A residue 911 VAL Chi-restraints excluded: chain A residue 914 ASN Chi-restraints excluded: chain A residue 931 ILE Chi-restraints excluded: chain A residue 934 ILE Chi-restraints excluded: chain A residue 957 GLN Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1082 CYS Chi-restraints excluded: chain A residue 1126 CYS Chi-restraints excluded: chain A residue 1128 VAL Chi-restraints excluded: chain C residue 66 HIS Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 176 LEU Chi-restraints excluded: chain C residue 189 LEU Chi-restraints excluded: chain C residue 198 ASP Chi-restraints excluded: chain C residue 207 HIS Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 237 ARG Chi-restraints excluded: chain C residue 291 CYS Chi-restraints excluded: chain C residue 305 SER Chi-restraints excluded: chain C residue 345 THR Chi-restraints excluded: chain C residue 346 ARG Chi-restraints excluded: chain C residue 351 TYR Chi-restraints excluded: chain C residue 385 THR Chi-restraints excluded: chain C residue 392 PHE Chi-restraints excluded: chain C residue 393 THR Chi-restraints excluded: chain C residue 395 VAL Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 456 PHE Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 458 LYS Chi-restraints excluded: chain C residue 461 LEU Chi-restraints excluded: chain C residue 468 ILE Chi-restraints excluded: chain C residue 483 VAL Chi-restraints excluded: chain C residue 497 PHE Chi-restraints excluded: chain C residue 516 GLU Chi-restraints excluded: chain C residue 524 VAL Chi-restraints excluded: chain C residue 559 PHE Chi-restraints excluded: chain C residue 569 ILE Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 615 VAL Chi-restraints excluded: chain C residue 754 LEU Chi-restraints excluded: chain C residue 878 LEU Chi-restraints excluded: chain C residue 884 SER Chi-restraints excluded: chain C residue 895 GLN Chi-restraints excluded: chain C residue 934 ILE Chi-restraints excluded: chain C residue 1001 LEU Chi-restraints excluded: chain C residue 1072 GLU Chi-restraints excluded: chain C residue 1075 PHE Chi-restraints excluded: chain C residue 1105 THR Chi-restraints excluded: chain C residue 1136 THR Chi-restraints excluded: chain C residue 1141 LEU Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 83 VAL Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 169 GLU Chi-restraints excluded: chain B residue 200 TYR Chi-restraints excluded: chain B residue 220 PHE Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 383 SER Chi-restraints excluded: chain B residue 478 THR Chi-restraints excluded: chain B residue 488 CYS Chi-restraints excluded: chain B residue 515 PHE Chi-restraints excluded: chain B residue 517 LEU Chi-restraints excluded: chain B residue 523 THR Chi-restraints excluded: chain B residue 547 THR Chi-restraints excluded: chain B residue 569 ILE Chi-restraints excluded: chain B residue 576 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 592 PHE Chi-restraints excluded: chain B residue 613 GLN Chi-restraints excluded: chain B residue 615 VAL Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 723 THR Chi-restraints excluded: chain B residue 732 THR Chi-restraints excluded: chain B residue 850 ILE Chi-restraints excluded: chain B residue 851 CYS Chi-restraints excluded: chain B residue 878 LEU Chi-restraints excluded: chain B residue 934 ILE Chi-restraints excluded: chain B residue 976 VAL Chi-restraints excluded: chain B residue 1004 LEU Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1029 MET Chi-restraints excluded: chain B residue 1031 GLU Chi-restraints excluded: chain B residue 1104 VAL Chi-restraints excluded: chain B residue 1145 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 301 random chunks: chunk 285 optimal weight: 0.8980 chunk 135 optimal weight: 10.0000 chunk 238 optimal weight: 8.9990 chunk 166 optimal weight: 2.9990 chunk 188 optimal weight: 1.9990 chunk 185 optimal weight: 2.9990 chunk 141 optimal weight: 0.6980 chunk 225 optimal weight: 0.8980 chunk 68 optimal weight: 0.5980 chunk 29 optimal weight: 20.0000 chunk 14 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 532 ASN C 907 ASN ** C1106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 907 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.177466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.109058 restraints weight = 30815.270| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.88 r_work: 0.3056 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 24920 Z= 0.137 Angle : 0.618 19.415 34025 Z= 0.296 Chirality : 0.047 0.618 4002 Planarity : 0.004 0.047 4310 Dihedral : 7.119 77.406 4362 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.37 % Allowed : 8.11 % Favored : 91.52 % Rotamer: Outliers : 5.16 % Allowed : 26.63 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.16), residues: 2961 helix: 2.27 (0.21), residues: 625 sheet: -0.85 (0.20), residues: 630 loop : -1.83 (0.15), residues: 1706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 319 TYR 0.013 0.001 TYR A1067 PHE 0.023 0.001 PHE B 238 TRP 0.009 0.001 TRP A 886 HIS 0.003 0.001 HIS A1064 Details of bonding type rmsd covalent geometry : bond 0.00329 (24832) covalent geometry : angle 0.57522 (33799) SS BOND : bond 0.00411 ( 38) SS BOND : angle 1.51094 ( 76) hydrogen bonds : bond 0.04015 ( 799) hydrogen bonds : angle 4.89574 ( 2199) link_BETA1-4 : bond 0.00378 ( 16) link_BETA1-4 : angle 1.93938 ( 48) link_NAG-ASN : bond 0.00569 ( 34) link_NAG-ASN : angle 3.77671 ( 102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6913.97 seconds wall clock time: 118 minutes 54.36 seconds (7134.36 seconds total)